Course catalogue doctoral education - VT24
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| Title | Mass spectrometry-based proteomics: When and How. |
|---|---|
| Course number | 2522 |
| Programme | 1-Included in several programmes |
| Language | English |
| Credits | 3.0 |
| Date | 2014-10-13 -- 2014-10-24 | Responsible KI department | Department of Oncology-Pathology |
| Specific entry requirements | |
| Intended learning outcomes | After completed the course, the student will be able to -Define and apply common proteomics terminology -Recognize the principles of the most common proteomics techniques -Understand the mass spectrometry based proteomics workflow: Experimental design, sample preparation and selection of techniques -Understand proteomics to such an extent that he/she will be able to utilize proteomics core facilities or collaborate with proteomics researchers. -Evaluate the quality of protein and peptide identifications. -Demonstrate how modern proteomics is applied to clinical research and to evaluate when proteomics research could be beneficial to incorporate in research projects. -Design their own research project by mass spectrometry based proteomics. |
| Contents of the course | The aim of this course is to give an overview of mass spectrometry based proteomics for researchers that will apply these techniques in their own research. Lectures and workshops on -Overview of proteomics -The proteomics workflow -Basic of separation sciences: Protein and peptides -Introduction to Mass spectrometry -Experimental design -Sample preparation, immunoprecipitation and enrichment strategy -Quantitative and qualitative proteomics by mass spectrometry -Global and targeted proteomics -Human protein atlas and Biological validation -Clinical applications A practical laboratory exercise using mass spectrometry based proteomics This course is focusing on proteomics technologies and applications, for proteomics data analysis we recommend our KI doctoral course ""Omics data analysis: From quantitative data to biological information"" |
| Teaching and learning activities | The course contains lectures, seminars, and a practical laboratory exercise using proteomics techniques. The students will plan their own project as a case study as well make an oral laboratory report. |
| Compulsory elements | -Attendance at lectures and the practical laboratory exercise. -Attendance at examination seminar and hand in the written examination assignment. -Extra written assignments can be used to compensate absence. The students are recommended to read literatures listed below in advance of the course. |
| Examination | -Students shall describe a proteomics project (beneficially related to their research) including different aspects from the proteomics workflow. This is handed in as a written exam. -The students shall perform an oral laboratory report |
| Literature and other teaching material | The students are recommended to read in advance of the course. (Will be listed on Course website: PingPong) * Matthias Mann, Nils A. Kulak, Nagarjuna Nagaraj, and Jurgen Cox. The Coming Age of Complete, Accurate, and Ubiquitous Proteomes. Molecular Cell 2013 49; 583-590. * F. Maarten Altelaar, Javier Munoz and Albert J. R. Heck. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genetics. 2013. 14; 35-48 * Cox J. and Mann M. Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology. Annu. Rev. Biochem. 2011. 80; 273-99 * Domon B. and Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol. 2010 28(7); 710-721. * Gstaiger M. and Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genetics. 2009. 10; 617-627 Supplementary literatures will help to understand lectures and design of your project: Will be listed on PingPong. |
| Number of students | 15 - 20 |
| Selection of students | Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given to earlier registration date) |
| More information | Please note that this is a full-time course and that both lectures and the practical part are compulsory. Please refer to the course site in ping pong for additional information http://pingpong.ki.se/public/courseId/9160/lang-sv/publicPage.do
This course is included in the doctoral programmes Allergy, immunology and inflammation (Aii) and Infection biology. See http://ki.se/en/education/doctoral-programmes. |
| Additional course leader | |
| Latest course evaluation | Course evaluation report |
| Course responsible |
Maria Pernemalm Department of Oncology-Pathology Maria.Pernemalm@ki.se |
| Contact person |
Maria Pernemalm Institutionen för onkologi-patologi Maria.Pernemalm@ki.se Hanna Kjellin Institutionen för molekylär medicin och kirurgi Hanna.Kjellin@ki.se |
